For focusing when trying to photograph birds in flight, I've more or less come to the following settings, but I'm still experimenting with the D4 and probably will be for several more months.
To start, for nature photography I have decoupled the shutter release from autofocus. Pressing the shutter release don't affect focusing. I activate autofocus via the AF-On button. This has been done so I can easily use autofocus to get close to or at optimum focus, and then if essential, finish with manual focus as necessary when focusing on stationary, or semi-stationary birds and other animals.
When I go from AFS to AFC, for flying birds, I don't change that. It's easy to use the AF-On button for all wildlife shooting.
So for panning for birds in flight:
Autofocus Mode: AFC AF Area Mode: 21-point dynamic-area AF Focus Point: Center (Locked)
a1 AF-C Priority Select: Release a3 Focus Track Lock-on: Off a4 AF Activation: Off (As mentioned above) a5 AF Point Illumination, Continuous focus mode: On a5 AF Point Illumination, Focus point brightness: 0 a5 AF Point Illumination, Dynamic-area AF display: On a6 Focus Point Wrap: On a7 Number of Focus Points: 51 a8 Assign AF-On Button: AF-On a9 Assign AF-On Button Vertical: AF-On a10 Store Points Orientation: On